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10 Active Transport of ATP, ADP, and Pi Across the Mitochondrial Membrane

10 Active Transport of ATP, ADP, and Pi Across the Mitochondrial Membrane

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elongation factor. A protein that is involved

in extending the peptide chain during protein synthesis.

enantiomers. Stereoisomers that are nonsuperimposable mirror images.

endocytosis. The process by which matter is

engulfed by a plasma membrane and brought

into the cell within a lipid vesicle derived

from the membrane.

endonuclease. An enzyme that catalyzes the

hydrolysis of phosphodiester linkages at various sites within polynucleotide chains.

endoplasmic reticulum. A membranous

network of tubules and sheets continuous

with the outer nuclear membrane of eukaryotic cells. Regions of the endoplasmic reticulum coated with ribosomes are called the

rough endoplasmic reticulum; regions having no attached ribosomes are known as the

smooth endoplasmic reticulum. The endoplasmic reticulum is involved in the sorting

and transport of certain proteins and in the

synthesis of lipids.

endosomes. Smooth vesicles inside the cell

that are receptacles for endocytosed material.

energy-rich compound. A compound whose

hydrolysis occurs with a large negative freeenergy change (equal to or greater than that

for ATP : ADP + Pi).

enthalpy (H). A thermodynamic state function that describes the heat content of a system.

entropy (S). A thermodynamic state function that describes the randomness or disorder of a system.

enzymatic reaction. A reaction catalyzed by

a biological catalyst, an enzyme. Enzymatic

reactions are 103 to 1017 times faster than the

corresponding uncatalyzed reactions.

enzyme. A biological catalyst, almost always

a protein. Some enzymes may require additional cofactors for activity. Virtually all biochemical reactions are catalyzed by specific


enzyme assay. A method used to analyze the

activity of a sample of an enzyme. Typically,

enzymatic activity is measured under selected

conditions such that the rate of conversion of

substrate to product is proportional to enzyme concentration.

enzyme inhibitor. A compound that binds

to an enzyme and interferes with its activity

by preventing either the formation of the ES

complex or its conversion to E + P.

enzyme-substrate complex (ES). A complex

formed when substrate molecules bind noncovalently within the active site of an


epimers. Isomers that differ in configuration

at only one of several chiral centers.

equilibrium. The state of a system in which

the rate of conversion of substrate to product

is equal to the rate of conversion of product

to substrate. The free-energy change for a reaction or system at equilibrium is zero.

equilibrium constant (Keq). The ratio of the

concentrations of products to the concentrations of reactants at equilibrium. The equilibrium constant is related to the standard

Gibbs free energy change of reaction.

essential amino acid. An amino acid that

cannot be synthesized by an animal and must

be obtained in the diet.

essential fatty acid. A fatty acid that cannot

be synthesized by an animal and must be obtained in the diet.

essential ion. An ion required as a cofactor

for the catalytic activity of certain enzymes.

Some essential ions, called activator ions, are

reversibly bound to enzymes and often participate in the binding of substrates, whereas

tightly bound metal ions frequently participate directly in catalytic reactions.

eukaryote. An organism whose cells generally possess a nucleus and internal membranes (cf., prokaryote).

excision repair. The reversal of DNA damage by excision-repair endonucleases. Gross

lesions that alter the structure of the DNA

helix are repaired by cleavage on each side of

the lesion and removal of the damaged DNA.

The resulting single-stranded gap is filled by

DNA polymerase and sealed by DNA ligase.

exocytosis. The process by which material

destined for secretion from a cell is enclosed

in lipid vesicles that are transported to and

fuse with the plasma membrane, releasing

the material into the extracellular space.

exon. A nucleotide sequence that is present

in the primary RNA transcript and in the

mature RNA molecule. The term exon also

refers to the region of the gene that corresponds to a sequence present in the mature

RNA (cf., intron).

exonuclease. An enzyme that catalyzes the

sequential hydrolysis of phosphodiester linkages from one end of a polynucleotide chain.

extrinsic membrane protein. See peripheral

membrane protein.

facilitated diffusion. See passive transport.

facultative anaerobe. An organism that can

survive in the presence or absence of oxygen.

fatty acid. A long chain aliphatic hydrocarbon with a single carboxyl group at one end.

Fatty acids are the simplest type of lipid and

are components of many more complex

lipids, including triacylglycerols, glycerophospholipids, sphingolipids, and waxes.

feedback inhibition. Inhibition of an enzyme that catalyzes an early step in a metabolic pathway by an end product of the same


feed-forward activation. Activation of an

enzyme in a metabolic pathway by a metabolite produced earlier in the pathway.

fermentation. The anaerobic catabolism of

metabolites for energy production. In alcoholic fermentation, pyruvate is converted to

ethanol and carbon dioxide.


fibrous proteins. A major class of water-insoluble proteins that associate to form long

fibers. Many fibrous proteins are physically

tough and provide mechanical support to individual cells or entire organisms.

first-order reaction. A reaction whose rate

is directly proportional to the concentration

of only one reactant.

Fischer projection. A two-dimensional representation of the three-dimensional structures of sugars and related compounds. In a

Fischer projection, the carbon skeleton is

drawn vertically, with C-1 at the top. At a chiral center, horizontal bonds extend toward

the viewer and vertical bonds extend away

from the viewer.

fluid mosaic model. A model proposed for

the structure of biological membranes. In

this model, the membrane is depicted as a dynamic structure in which lipids and membrane proteins (both integral and peripheral)

rotate and undergo lateral diffusion.

fluorescence. A form of luminescence in

which visible radiation is emitted from a

molecule as it passes from a higher to a lower

electronic state.

flux. The flow of material through a metabolic pathway. Flux depends on the supply of

substrates, the removal of products, and the

catalytic capabilities of the enzymes involved

in the pathway.

fold. A combination of secondary structures

that form the core of a protein domain. Many

different folds have been characterized.

frameshift mutation. An alteration in DNA

caused by the insertion or deletion of a number of nucleotides not divisible by three. A

frameshift mutation changes the reading

frame of the corresponding mRNA molecule

and affects translation of all codons downstream of the mutation.

free energy change. See Gibbs free energy


free radical. A molecule or atom with an

unpaired electron.

furanose. A monosaccharide structure that

forms a five-membered ring as a result of intramolecular hemiacetal formation.

G protein. A protein that binds guanine nucleotides.

≤G. See Gibbs free energy change.

≤G° œ . See standard Gibbs free energy change.

ganglioside. A glycosphingolipid in which

oligosaccharide chains containing N-acetylneuraminic acid are attached to a ceramide.

Gangliosides are present on cell surfaces and

provide cells with distinguishing surface

markers that may serve in cellular recognition and cell-to-cell communication.

gas chromatography. A chromatographic

technique used to separate components of a

mixture based on their partitioning between

the gas phase and a stationary phase, which

can be a liquid or solid.



gel-filtration chromatography. A chromatographic technique used to separate a mixture

of proteins or other macromolecules in solution based on molecular size, using a matrix of

porous beads. Also known as molecular-exclusion chromatography.

gene. Loosely defined as a segment of DNA

that is transcribed. In some cases, the term

gene may also be used to refer to a segment of

DNA that encodes a functional protein or

corresponds to a mature RNA molecule.

genetic code. The correspondence between

a particular three nucleotide codon and the

amino acid it specifies. The standard genetic

code of 64 codons is used by almost all organisms. The genetic code is used to translate

the sequence of nucleotides in mRNA into


genetic recombination. The exchange or

transfer of DNA from one molecule of DNA

to another (cf., homologous recombination).

genome. One complete set of the genetic information in an organism. It may be a single

chromosome or a set of chromosomes (haploid). Mitochondria and chloroplasts have

genomes separate from that in the nucleus of

eukaryotic cells.

Gibbs free energy change (≤G). A thermodynamic quantity that defines the equilibrium condition in terms of the changes in

enthalpy (H) and entropy (S) of a system at

constant pressure. ¢G = ¢H - T¢S, where

T is absolute temperature. Free energy is a

measure of the energy available within a system to do work.

globular proteins. A major class of proteins,

many of which are water soluble. Globular

proteins are compact and roughly spherical,

containing tightly folded polypeptide chains.

Typically, globular proteins include indentations, or clefts that specifically recognize and

transiently bind other compounds.

glucogenic compound. A compound, such

as an amino acid, that can be used for gluconeogenesis in animals.

gluconeogenesis. A pathway for synthesis of

glucose from a noncarbohydrate precursor.

Gluconeogenesis from pyruvate involves the

seven near-equilibrium reactions of glycolysis traversed in the reverse direction. The

three metabolically irreversible reactions of

glycolysis are bypassed by four enzymatic reactions that do not occur in glycolysis.

glucoside. A glycoside where the anomeric

carbon atom is from glucose.

glycan. A general term for an oligosaccharide

or a polysaccharide. A homoglycan is a polymer of identical monosaccharide residues; a

heteroglycan is a polymer of different monosaccharide residues.

glycerophospholipid. A lipid consisting of

two fatty acyl groups bound to C-1 and C-2 of

glycerol 3-phosphate and, in most cases, a

polar substituent attached to the phosphate

moiety. Glycerophospholipids are major components of biological membranes.

glycoconjugate. A carbohydrate derivative

in which one or more carbohydrate chains

are covalently linked to a peptide chain, protein, or lipid.

glycoforms. Glycoproteins containing identical amino acid sequences but different

oligosaccharide-chain compositions.

glycogen. A branched homopolymer of glucose residues joined by a-(1 : 4) linkages

with a-(1 : 6) linkages at branch points.

Glycogen is a storage polysaccharide in animals and bacteria.

glycolysis. A catabolic pathway consisting of

10 enzyme-catalyzed reactions by which one

molecule of glucose is converted to two molecules of pyruvate. In the process, two molecules

of ATP are formed from ADP + Pi, and two

molecules of NAD1 are reduced to NADH.

glycoprotein. A protein that contains covalently bound carbohydrate residues.

glycosaminoglycan. An unbranched polysaccharide of repeating disaccharide units.

One component of the disaccharide is an

amino sugar; the other component is usually

a uronic acid.

glycoside. A molecule containing a carbohydrate in which the hydroxyl group of the

anomeric carbon has been replaced through

condensation with an alcohol, an amine, or a


glycosidic bond. Acetal linkage formed by

condensation of the anomeric carbon atom

of a saccharide with a hydroxyl, amino, or

thiol group of another molecule. The most

commonly encountered glycosidic bonds are

formed between the anomeric carbon of one

sugar and a hydroxyl group of another sugar.

Nucleosidic bonds are N-linked glycosidic


glycosphingolipid. A



sphingosine and carbohydrate moieties.

glycosylation. See protein glycosylation.

glyoxylate cycle. A variation of the citric

acid cycle in certain plants, bacteria, and

yeast that allows net production of glucose

from acetyl CoA via oxaloacetate. The glyoxylate cycle bypasses the two CO22 producing steps of the citric acid cycle.

glyoxysome. An organelle that contains specialized enzymes for the glyoxylate cycle.

Golgi apparatus. A complex of flattened,

fluid-filled membranous sacs in eukaryotic

cells, often found in proximity to the endoplasmic reticulum. The Golgi apparatus is

involved in the modification, sorting, and

targeting of proteins.

granum. A stack of flattened vesicles formed

from the thylakoid membrane in chloroplasts.

group transfer potential. See photsphoryl

group transfer potential.

group transfer reaction. A reaction in

which a substituent or functional group is

transferred from one substrate to another.

H. See enthalpy.

hairpin. 1. A secondary structure adopted by

single-stranded polynucleotides that arises

when short regions fold back on themselves

and hydrogen bonds form between complementary bases. Also known as a stem-loop.

2. A tight turn connecting two consecutive

b strands of a polypeptide.

haploid. Having one set of chromosomes or

one copy of the genome (cf., diploid).

high energy molecule. See energy-rich


Haworth projection. A representation in

which a cyclic sugar molecule is depicted as a

flat ring that is projected perpendicular to the

plane of the page. Heavy lines represent the

part of the molecule that extends toward the


HDL. See high density lipoprotein.

heat of vaporization. The amount of heat

required to evaporate 1 gram of a liquid.

heat shock protein. A protein whose synthesis is increased in response to stresses such as

high temperature. Many heat shock proteins

are chaperones that are also expressed in the

absence of stress.

helicase. An enzyme that is involved in unwinding DNA.

hemiacetal. The product formed when an

alcohol reacts with an aldehyde.

hemiketal. The product formed when an alcohol reacts with a ketone.

Henderson-Hasselbalch equation. An equation that describes the pH of a solution of a

weak acid or a weak base in terms of the pKa

and the concentrations of the proton donor

and proton acceptor forms.

heterochromatin. Regions of chromatin

that are highly condensed.

heterocyclic molecule. A molecule that contains a ring structure made up of more than

one type of atom.

heteroglycan (heteropolysaccharide). A carbohydrate polymer whose residues consist of

two or more different types of monosaccharide.

heterotroph. An organism that requires at

least one organic nutrient, such as glucose, as

a carbon source.

high density lipoprotein (HDL). A type of

plasma lipoprotein that is enriched in protein

and transports cholesterol and cholesteryl esters from tissues to the liver.

high-performance liquid chromatography

(HPLC). A chromatographic technique used

to separate components of a mixture by

dissolving the mixture in a liquid solvent and

forcing it to flow through a chromatographic

column under high pressure.

histones. A class of proteins that bind to

DNA to form chromatin. The nuclei of eukaryotic cells contain five histones, known as

H1, H2A, H2B, H3, and H4.

Holliday junction. The region of strand

crossover resulting from recombination between two molecules of homologous doublestranded DNA.


homoglycan (homopolysaccharide). A carbohydrate polymer whose residues consist of

a single type of monosaccharide.

homologous. Referring to genes or proteins

that descend from a common ancestor.

homologous recombination. Recombination

between molecules of DNA that have closely

related sequences (i.e., they are homologous).

This is the standard form of recombination

that occurs between chromosomes in eukaryotic cells.

homology. The similarity of genes or proteins as a result of evolution from a common


hormone response element. A DNA sequence that binds a transcriptional activator

consisting of a steroid hormone receptor


housekeeping genes. Genes that encode

proteins or RNA molecules that are essential

for the normal activities of all living cells.

HPLC. See high-performance liquid chromatography.

hydration. A state in which a molecule or

ion is surrounded by water.

hydrogen bond. A weak electrostatic interaction the formed when a hydrogen atom bonded

covalently to a strongly electronegative atom

is partially shared by interacting with electron

pair of another electronegative atom.

hydrolase. An enzyme that catalyzes the

hydrolytic cleavage of its substrate(s) (i.e.,


hydropathy. A measure of the hydrophobicity of amino acid side chains. The more positive the hydropathy value, the greater the


hydrophilic. “Water


molecules that interact favorably with water.

hydrophilicity. The degree to which a compound or functional group interacts with

water or is preferentially soluble in water.

hydrophobic. “Water fearing”—describing

molecules that do not interact favorably with

water and are much less soluble than hydrophilic molecules.

hydrophobic effect. The exclusion of hydrophobic groups or molecules by water. The

hydrophobic effect appears to depend on the

increase in entropy of solvent water molecules that are released from an ordered

arrangement around the hydrophobic group.

hydrophobic interaction. A weak, noncovalent interaction between nonpolar molecules

or substituents that results from the strong

association of water molecules with one another. Such association leads to the shielding

or exclusion of nonpolar molecules from an

aqueous environment.

hydrophobicity. The degree to which a

compound or functional group that is soluble in nonpolar solvents is insoluble or only

sparingly soluble in water.

IDL. See intermediate density lipoprotein.

induced fit. Activation of an enzyme by a

substrate-initiated conformational change.

inducer. A ligand that binds to and inactivates

a repressor thereby increasing the transcription

of the gene controlled by the repressor.

inhibition constant (Ki). The equilibrium

constant for the dissociation of an inhibitor

from an enzyme-inhibitor complex.

inhibitor. A compound that binds to an enzyme and inhibits its activity.

initial velocity (v0). The rate of conversion

of substrate to product in the early stages of

an enzymatic reaction, before appreciable

product has been formed.

initiation codon. A codon that specifies the

initiation site for protein synthesis. The methionine codon (AUG) is the most common

initiation codon.

initiation factor. See translation initiation


initiator tRNA. The tRNA molecule that is

used exclusively at initiation codons. The

initiator tRNA is usually a specific methionyl-tRNA.

integral membrane protein. A membrane

protein that penetrates the hydrophobic core

of the lipid bilayer and usually spans the bilayer completely. Also known as an intrinsic

membrane protein.

intercalating agent. A compound containing a planar ring structure that can fit between the stacked base pairs of DNA.

Intercalating agents distort the DNA structure, partially unwinding the double helix.

intermediary metabolism. The metabolic

reactions by which the small molecules of

cells are interconverted.

intermediate density lipoprotein (IDL). A

type of plasma lipoprotein that is formed

during the breakdown of VLDLs.

intermediate filament. A structure composed of different protein subunits, found in

the cytoplasm of most eukaryotic cells. Intermediate filaments are components of the cytoskeletal network.

intron. An internal nucleotide sequence that

is removed from the primary RNA transcript

during processing. The term intron also

refers to the region of the gene that corresponds to the corresponding RNA intron

(cf., exon).

inverted repeat. A sequence of nucleotides

that is repeated in the opposite orientation

within the same polynucleotide strand. An

inverted repeat in double-stranded DNA can

give rise to a cruciform structure.

ion pair. An electrostatic interaction between

ionic groups of opposite charge within the interior of a macromolecule such as a globular


ion product for water (Kw). The product of

the concentrations of hydronium ions and

hydroxide ions in an aqueous solution, equal

to 1.0 * 10 - 14 M2.

ion-exchange chromatography. A chromatographic technique used to separate a mixture of


ionic species in solution, using a charged matrix. In anion-exchange chromatography, a

positively charged matrix binds negatively

charged solutes, and in cation-exchange chromatography, a negatively charged matrix binds

positively charged solutes. The bound species

can be serially eluted from the matrix by gradually changing the pH or increasing the salt

concentration in the solvent.

ionophore. A compound that facilitates the

diffusion of ions across bilayers and membranes by serving as a mobile ion carrier or

by forming a channel for ion passage.

irreversible enzyme inhibition. A form of

enzyme inhibition where the inhibitor binds

covalently to the enzyme.

isoacceptor tRNA molecules. Different tRNA

molecules that bind the same amino acid.

isoelectric focusing. A modified form of

electrophoresis that uses buffers to create a

pH gradient within a polyacrylamide gel.

Each protein migrates to its isoelectric point

(pI), that is, the pH in the gradient at which it

no longer carries a net positive or negative


isoelectric point (pI). The pH at which a

zwitterionic molecule does not migrate in an

electric field because its net charge is zero.

isoenzymes. See isozymes.

isomerase. An enzyme that catalyzes an isomerization reaction, a change in geometry or

structure within one molecule.

isoprene. A branched, unsaturated five-carbon molecule that forms the basic structural

unit of all isoprenoids, including the steroids

and lipid vitamins.

isoprenoid. A lipid that is structurally related

to isoprene.

isozymes. Different proteins from a single

biological species that catalyze the same reaction. Also known as isoenzymes.

junk DNA. Regions of the genome with no

known function.

Ka. See acid dissociation constant.

kb. See kilobase pair.

kcat. See catalytic constant.

kcat>K m. The second-order rate constant

for conversion of enzyme and substrate to

enzyme and product at low substrate concentrations. The ratio of kcat to Km, when

used to compare several substrates, is called

the specificity constant.

Keq. See equilibrium constant.

ketogenesis. The pathway that synthesizes

ketone bodies from acetyl CoA in the mitochondrial matrix in mammals.

ketogenic compound. A compound, such as

an amino acid, that can be degraded to form

acetyl CoA and can thereby contribute to the

synthesis of fatty acids or ketone bodies.

ketone bodies. Small molecules that are

synthesized in the liver from acetyl CoA.

During starvation, the ketone bodies

b-hydroxybutyrate and acetoacetate become

major metabolic fuels.



ketoses. A class of monosaccharides in which

the most oxidized carbon atom, usually C-2,

is ketonic.

Kj. See inhibition constant.

kilobase pair (kb). A unit of length of double-stranded DNA, equivalent to 1000 base


kinase. An enzyme that catalyzes transfer of

a phosphoryl group to an acceptor molecule.

A protein kinase catalyzes the phosphorylation of protein substrates. Kinases are also

known as phosphotransferases.

kinetic mechanism. A scheme used to describe the sequence of steps in a multisubstrate enzyme-catalyzed reaction.

kinetic order. The sum of the exponents in a

rate equation, which reflects how many molecules are reacting in the slowest step of the

reaction. Also known as reaction order.

Km. See Michaelis constant.

Krebs cycle. See citric acid cycle.

Kw. See ion product of water.

lagging strand. The newly synthesized DNA

strand formed by discontinuous 5¿ : 3¿

polymerization in the direction opposite

replication fork movement.

lateral diffusion. The rapid motion of lipid

or protein molecules within the plane of one

leaflet of a lipid bilayer.

LDL. See low density lipoprotein.

leader peptide. The peptide encoded by a portion of the leader region of certain regulated

operons. Synthesis of a leader peptide is the

basis for regulating transcription of the entire

operon by the mechanism of attenuation.

leader region. The sequence of nucleotides

that lie between the transcription start site

and the first coding region of an operon.

leading strand. The newly synthesized DNA

strand formed by continuous 5¿ : 3¿ polymerization in the same direction as replication fork movement.

leaflet. One layer of a lipid bilayer.

lectin. A plant protein that binds specific

saccharides in glycoproteins.

leucine zipper. A structural motif found in

DNA-binding proteins and other proteins.

The zipper is formed when the hydrophobic

faces (frequently containing leucine residues)

of two amphipathic a-helices from the same

or different polypeptide chains interact to

form a coiled-coil structure.

LHC. See light-harvesting complex.

ligand. A molecule, group, or ion that binds

noncovalently to another molecule or atom.

ligand-gated ion channel. A membrane ion

channel that opens or closes in response to

binding of a specific ligand.

ligase. An enzyme that catalyzes the joining,

or ligation, of two substrates. Ligation reactions require the input of the chemical potential energy of a nucleoside triphosphate such

as ATP. Ligases are commonly referred to as


light reactions. The photosynthetic reactions in which protons derived from water

are used in the chemiosmotic synthesis of

ATP from ADP + Pi and a hydride ion from

water reduces to NADPH. Also known as the

light-dependent reactions.

light-harvesting complex (LHC). A large

pigment complex in the thylakoid membrane

that aids a photosystem in gathering light.

limit dextrin. A branched oligosaccharide

derived from a glucose polysaccharide by the

hydrolytic action of amylase or the phosphorolytic action of glycogen phosphorylase or

starch phosphorylase. Limit dextrins are resistant to further degradation catalyzed by

amylase or phosphorylase. Limit dextrins can

be further degraded only after hydrolysis of

the a-(1 : 6) linkages.

Lineweaver-Burk plot. See double-reciprocal


linker DNA. The stretch of DNA (approximately 54 base pairs) between two adjacent

nucleosome core particles.

lipase. An enzyme that catalyzes the hydrolysis of triacylglycerols.

lipid. A water-insoluble (or sparingly soluble) organic compound found in biological

systems, which can be extracted by using relatively nonpolar organic solvents.

lipid bilayer. A double layer of lipids in

which the hydrophobic tails associate with

one another in the interior of the bilayer and

the polar head groups face outward into the

aqueous environment. Lipid bilayers are the

structural basis of biological membranes.

lipid raft. A patch of membrane rich in cholesterol and sphingolipid.

lipid vitamin. A polyprenyl compound composed primarily of a long hydrocarbon chain

or fused ring. Unlike water-soluble vitamins,

lipid vitamins can be stored by animals. Lipid

vitamins include vitamins A, D, E, and K.

lipid anchored membrane protein. A membrane protein that is tethered to a membrane through covalent linkage to a lipid


lipopolysaccharide. A macromolecule composed of lipid A (a disaccharide of phosphorylated glucosamine residues with attached fatty

acids) and a polysaccharide. Lipopolysaccharides are found in the outer membrane of

gram-negative bacteria. These compounds are

released from bacteria undergoing lysis and

are toxic to humans and other animals. Also

known as an endotoxin.

lipoprotein. A macromolecular assembly of

lipid and protein molecules with a hydrophobic core and a hydrophilic surface. Lipids are

transported via lipoproteins.

liposome. A synthetic vesicle composed of a

phospholipid bilayer that encloses an aqueous compartment.

loop. A nonrepetitive polypeptide region

that connects secondary structures within a

protein molecule and provides directional

changes necessary for a globular protein to

attain its compact shape. Loops contain from

2 to 16 residues. Short loops of up to 5

residues are often called turns.

low density lipoprotein (LDL). A type of

plasma lipoprotein that is formed during the

breakdown of IDLs and is enriched in cholesterol and cholesteryl esters.

lumen. The aqueous space enclosed by a biological membrane, such as the membrane of

the endoplasmic reticulum or the thylakoid


lyase. An enzyme that catalyzes a nonhydrolytic or nonoxidative elimination reaction,

or lysis, of a substrate, with the generation of a

double bond. In the reverse direction, a lyase

catalyzes addition of one substrate to a double

bond of a second substrate.

lysophosphoglyceride. An


lipid that is produced when one of the two

fatty acyl moieties of a glycerophospholipid is

hydrolytically removed. Low concentrations

of lysophosphoglycerides are metabolic intermediates, whereas high concentrations

disrupt membranes, causing cells to lyse.

lysosome. A specialized digestive organelle

in eukaryotic cells. Lysosomes contain a variety of enzymes that catalyze the breakdown

of cellular biopolymers, such as proteins, nucleic acids, and polysaccharides, and the digestion of large particles, such as some

bacteria ingested by the cell.

major groove. The wide groove on the surface of a DNA double helix created by the

stacking of base pairs and the resulting twist

in the sugar-phosphate backbones.

MALDI. See matrix-assisted laser desorption ionization.

mass action ratio (Q). The ratio of the concentrations of products to the concentrations

of reactants of a reaction.

mass spectrometry. A technique that determines the mass of a molecule.

matrix. See mitochondrial matrix.

matrix-assisted laser desorption ionization

(MALDI). A technique in mass spectrometry where the target molecule is released from

a solid matrix by a laser beam.

maximum velocity (Vmax). The initial velocity of a reaction when the enzyme is saturated

with substrate, that is, when all the enzyme is

in the form of an enzyme-substrate complex.

melting curve. A plot of the change in absorbance versus temperature for a DNA molecule. The change in absorbance indicates

unfolding of the double helix.

melting point (Tm). The midpoint of the

temperature range in which double-stranded

DNA is converted to single-stranded DNA or

a protein is converted from its native form to

the denatured state.

membrane. A lipid bilayer containing associated proteins that serves to delineate and compartmentalize cells or organelles. Biological

membranes are also the site of many important


biochemical processes related to energy transduction and intracellular signaling.

membrane-associated electron transport.

See electron transport.

membrane potential (≤C). The charge separation across a membrane that results from

differences in ionic concentrations on the

two sides of the membrane.

messenger ribonucleic acid. See mRNA.

metabolic fuel. A small compound that can

be catabolized to release energy. In multicellular organisms, metabolic fuels may be transported between tissues.

metabolically irreversible reaction. A reaction in which the value of the mass action

ratio is two or more orders of magnitude

smaller than the value of the equilibrium

constant. The Gibbs free energy change for

such a reaction is a large negative number;

thus, the reaction is essentially irreversible.

metabolism. The sum total of biochemical

reactions carried out by an organism.

metabolite. An intermediate in the synthesis

or degradation of biopolymers and their

component units.

metabolite channeling. Transfer of the

product of one reaction of a multifunctional

enzyme or a multienzyme complex directly

to the next active site or enzyme without entering the bulk solvent. Channeling increases

the rate of a reaction pathway by decreasing

the transit time for an intermediate to reach

the next enzyme and by producing high local

concentrations of the intermediate.

metalloenzyme. An enzyme that contains

one or more firmly bound metal ions. In

some cases, such metal ions constitute part of

the active site of the enzyme and are active

participants in catalysis.

micelle. An aggregation of amphipathic

molecules in which the hydrophilic portions

of the molecules project into the aqueous

environment and the hydrophobic portions

associated with one another in the interior of

the structure to minimize contact with water


Michaelis constant (Km). The concentration of substrate that results in an initial

velocity (v0) equal to one-half the maximum

velocity (Vmax) for a given reaction.

Michaelis-Menten equation. A rate equation

relating the initial velocity (v0) of an enzymatic reaction to the substrate concentration

([S]), the maximum velocity (Vmax), and the

Michaelis constant (Km).

microfilament. See actin filament.

microtubule. A protein filament composed

of a and b tubulin heterodimers. Microtubules are components of the cytoskeletal

network and can form structures capable of

directed movement.

minor groove. The narrow groove on the

surface of a DNA double helix created by the

stacking of base pairs and the resulting twist

in the sugar-phosphate backbones.

mismatch repair. Restoration of the normal

nucleotide sequence in a DNA molecule containing mismatched bases. In mismatch repair, the correct strand is recognized, a

portion of the incorrect strand is excised, and

correctly base-paired, double-stranded DNA

is synthesized by the actions of DNA polymerase and DNA ligase.

missense mutation. An alteration in DNA

that involves the substitution of one nucleotide for another, resulting in a change in

the amino acid specified by that codon.

mitochondrial matrix. The gel-like phase

enclosed by the inner membrane of the mitochondrion. The mitochondrial matrix contains many enzymes involved in aerobic

energy metabolism.

mitochondrion. An organelle that is the

main site of oxidative energy metabolism in

most eukaryotic cells. Mitochondria contain

an outer and an inner membrane, the latter

characteristically folded into cristae.

mixed inhibition. A form of enzyme inhibition where both Km and Vmax are affected.

molar mass. The weight in grams of one

mole of a compound.

molecular chaperone. See chaperone.

molecular crowding. The decrease in diffusion rate that occurs when molecules collide

with each other.

molecular weight. See relative molecular


monocistronic mRNA. An mRNA molecule

that encodes only a single polypeptide. Most

eukaryotic mRNA molecules are monocistronic.

monomer. 1. A small compound that becomes a residue when polymerized with

other monomers. 2. A single subunit of a

multisubunit protein.

monosaccharide. A simple sugar of three or

more carbon atoms with the empirical formula (CH2O)n.

monounsaturated fatty acid. An unsaturated

fatty acid with a single carbon-carbon double


motif. A combination of secondary structure

that appears in a number of different proteins.

Also known as supersecondary structure.

Mr. See relative molecular mass.

mRNA. A class of RNA molecules that serve

as templates for protein synthesis.

mRNA precursor. A class of RNA molecules

synthesized by eukaryotic RNA polymerase

II. mRNA precursors are processed posttranscriptionally to produce mature messenger


mucin. A high-molecular-weight O-linked

glycoprotein containing as much as 80% carbohydrate by mass. Mucins are extended,

negatively charged molecules that contribute

to the viscosity of mucus, the fluid found on

the surfaces of the gastrointestinal, genitourinary, and respiratory tracts.


multienzyme complex. An oligomeric protein that catalyzes several metabolic reactions.

mutagen. An agent that can cause DNA


mutation. A heritable change in the sequence of nucleotides in DNA that causes a

permanent alteration of genetic information.

near-equilibrium reaction. A reaction in

which the value of the mass action ratio is

close to the value of the equilibrium constant.

The Gibbs free energy change for such a reaction is small; thus, the reaction is reversible.

Nernst equation. An equation that relates

the observed change in reduction potential

(¢E) to the change in standard reduction potential (¢E°¿) of a reaction.

neutral phospholipids. Glycerophospholipids,

such as phosphatidyl choline, having no net


neutral solution. An aqueous solution that

has a pH value of 7.0.

nick translation. The process in which DNA

polymerase binds to a gap between the 3¿ end

of a nascent DNA chain and the 5¿ end of the

next RNA primer, catalyzes hydrolytic removal of ribonucleotides using 5¿ : 3¿ exonuclease activity, and replaces them with

deoxyribonucleotides using 5¿ : 3¿ polymerase activity.

nitrogen cycle. The flow of nitrogen from

N2 to nitrogen oxides (NO2ᮎ and NO3ᮎ ) ammonia, nitrogenous biomolecules, and back

to N2.

nitrogen fixation. The reduction of atmospheric nitrogen to ammonia. Biological nitrogen fixation occurs in only a few species of

bacteria and algae.

N-linked oligosaccharide. An oligosaccharide chain attached to a protein through covalent bonds to the amide nitrogen atom of

side chain of asparagine residues. The

oligosaccharide chains of N-linked glycoproteins contain a core pentasaccharide of two

N-acetylglucosamine residues and three

mannose residues.

NMR spectroscopy. See nuclear magnetic

resonance spectroscopy.

noncompetitive inhibition. Inhibition of an

enzyme-catalyzed reaction by a reversible inhibitor that binds to either the enzyme or the

enzyme- substrate complex.

nonessential amino acid. An amino acid

that an animal can produce in sufficient

quantity to meet metabolic needs.

nonhomologous recombination. Recombination between unrelated sequences that do not

share significant sequence similarity.

nonrepetitive structure. An element of protein structure in which consecutive residues

do not have a single repeating conformation.

nonsense mutation. An alteration in DNA

that involves the substitution of one nucleotide for another, changing a codon that

specifies an amino acid to a termination



codon. A nonsense mutation results in premature termination of a protein’s synthesis.

N-terminus. The amino acid residue bearing a free a-amino group at one end of a peptide chain. In some proteins, the N-terminus

is blocked by acylation. The N-terminal

residue is usually assigned the residue number 1. Also known as the amino terminus.

nuclear envelope. The double membrane

that surrounds the nucleus and contains protein-lined nuclear pore complexes that regulate the import and export of material to and

from the nucleus. The outer membrane of

the nuclear envelope is continuous with the

endoplasmic reticulum; the inner membrane

is lined with filamentous proteins, constituting the nuclear lamina.

nuclear magnetic resonance spectroscopy

(NMR spectroscopy). A technique used to

study the structures of molecules in solution.

In nuclear magnetic resonance spectroscopy,

the absorption of electromagnetic radiation

by molecules in magnetic fields of varying

frequencies is used to determine the spin

states of certain atomic nuclei.

nuclease. An enzyme that catalyzes hydrolysis of the phosphodiester linkages of a

polynucleotide chain. Nucleases can be classified as endonucleases and exonucleases.

nucleic acid. A polymer composed of nucleotide residues linked in a linear sequence

by 3¿ –5¿ phosphodiester linkages. DNA and

RNA are nucleic acids composed of deoxyribonucleotide residues and ribonucleotide

residues, respectively.

nucleoid region. The region within a prokaryotic cell that contains the chromosome.

nucleolus. The region of the eukaryotic nucleus where rRNA transcripts are processed

and ribosomes are assembled.

nucleophile. An electron-rich species that is

negatively charged or contains unshared electron pairs and is attracted to chemical species

that are positively charged or electron-deficient (electrophiles).

nucleophilic substitution. A reaction in

which one nucleophile (e.g., Y ᮎ ) displaces

another (e.g., X ᮎ ).

nucleoside. A purine or pyrimidine N-glycoside of ribose or deoxyribose.

nucleosome. A DNA-protein complex that

forms the fundamental unit of chromatin. A

nucleosome consists of a nucleosome core

particle (approximately 146 base pairs of

DNA plus a histone octamer), linker DNA

(approximately 54 base pairs), and histone

H1 (which binds the core particle and linker


nucleosome core particle. A DNA-protein

complex composed of approximately 146

base pairs of DNA wrapped around an octamer of histones (two each of H2A, H2B,

H3, and H4).

nucleotide. The phosphate ester of a nucleoside, consisting of a nitrogenous base linked

to a pentose phosphate. Nucleotides are the

monomeric units of nucleic acids.

nucleus. An organelle that contains the

principal genetic material of eukaryotic cells

and functions as the major site of RNA synthesis and processing.

obligate aerobe. An organism that requires

the presence of oxygen for survival.

obligate anaerobe. An organism that requires

an oxygen-free environment for survival.

Okazaki fragments. Relatively short strands

of DNA that are produced during discontinuous synthesis of the lagging strand of DNA.

oligomer. A multisubunit molecule whose

arrangement of subunits always has a defined

stoichiometry and almost always displays


oligonucleotide. A polymer of several (up to

about 20) nucleotide residues linked by phosphodiester bonds.

oligopeptide. A polymer of several (up to

about 20) amino acid residues linked by

peptide bonds.

oligosaccharide. A polymer of 2 to about 20

monosaccharide residues linked by glycosidic


oligosaccharide processing. The enzymecatalyzed addition and removal of saccharide

residues during the maturation of a glycoprotein.

O-linked oligosaccharide. An oligosaccharide attached to a protein through a covalent

bond to the hydroxyl oxygen atom of a serine

or threonine residue.

open reading frame. A stretch of nucleotide

triplets that contains no termination codons.

Protein-encoding regions are examples of

open reading frames.

operator. A DNA sequence to which a specific repressor protein binds, thereby blocking transcription of a gene or operon.

operon. A bacterial transcriptional unit

consisting of several different coding regions

cotranscribed from one promoter.

ordered sequential reaction. A reaction in

which both the binding of substrates to an

enzyme and the release of products from the

enzyme follow an obligatory order.

organelle. Any specialized membranebounded structure within a eukaryotic cell.

Organelles are uniquely organized to perform specific functions.

origin of replication. A DNA sequence at

which replication is initiated.

osmosis. The movement of solvent molecules from a less concentrated solution to an

adjacent, more concentrated solution.

osmotic pressure. The pressure required to

prevent the flow of solvent from a less concentrated solution to a more concentrated


oxidase. An enzyme that catalyzes an oxidation-reduction reaction in which O2 is the

electron acceptor. Oxidases are members of

the IUBMB class of enzymes known as oxidoreductases.

oxidation. The loss of electrons from a substance through transfer to another substance

(the oxidizing agent). Oxidations can take

several forms, including the addition of oxygen to a compound, the removal of hydrogen

from a compound to create a double bond, or

an increase in the valence of a metal ion.

oxidative phosphorylation. See electron


oxidizing agent. A substance that accepts

electrons in an oxidation-reduction reaction

and thereby becomes reduced.

oxidoreductase. An enzyme that catalyzes an

oxidation-reduction reaction. Some oxidoreductases are known as dehydrogenases, oxidases, peroxidases, oxygenases, or reductases.

oxygenation. The reversible binding of oxygen to a macromolecule.

≤p. See protonmotive force.

PAGE. See polyacrylamide gel electrophoresis.

passive transport. The process by which a

solute specifically binds to a transport protein and is transported across a membrane,

moving with the solute concentration gradient. Passive transport occurs without the expenditure of energy. Also known as facilitated


Pasteur effect. The slowing of glycolysis in

the presence of oxygen.

pathway. A sequence of metabolic reactions.

pause site. A region of a gene where transcription slows. Pausing is exaggerated at

palindromic sequences, where newly synthesized RNA can form a hairpin structure.

PCR. See polymerase chain reaction.

pentose phosphate pathway. A pathway by

which glucose 6-phosphate is metabolized to

generate NADPH and ribose 5-phosphate. In

the oxidative stage of the pathway, glucose 6phosphate is converted to ribulose 5-phosphate

and CO2 rating two molecules of NADPH. In

the nonoxidative stage, ribulose 5-phosphate

can be isomerized to ribose 5-phosphate or

converted to intermediates of glycolysis. Also

known as the hexose monophosphate shunt.

peptide. Two or more amino acids covalently

joined in a linear sequence by peptide bonds.

peptide bond. The covalent secondary

amide linkage that joins the carbonyl group

of one amino acid residue to the amino nitrogen of another in peptides and proteins.

peptide group. The nitrogen and carbon

atoms involved in a peptide bond and their

four substituents: the carbonyl oxygen atom,

the amide hydrogen atom, and the two adjacent a-carbon atoms.

peptidoglycan. A macromolecule containing a heteroglycan chain of alternating Nacetylglucosamine and N-acetylmuramic

acid cross-linked to peptides of varied composition. Peptidoglycans are the major components of the cell walls of many bacteria.

peptidyl site. See P site.


peptidyl transferase. The enzymatic activity

responsible for the formation of a peptide

bond during protein synthesis.

peptidyl-tRNA. The tRNA molecule to

which the growing peptide chain is attached

during protein synthesis.

peripheral membrane protein. A membrane

protein that is weakly bound to the interior or

exterior surface of a membrane through ionic

interactions and hydrogen bonding with the

polar heads of the membrane lipids or with an

integral membrane protein. Also known as an

extrinsic membrane protein.

periplasmic space. The region between the

plasma membrane and the cell wall in bacteria.

permeability coefficient. A measure of the

ability of an ion or small molecule to diffuse

across a lipid bilayer.

peroxisome. An organelle in all animal and

many plant cells that carries out oxidation reactions, some of which produce the toxic

compound hydrogen peroxide (H2O2). Peroxisomes contain the enzyme catalase, which

catalyzes the breakdown of toxic H2O2 to

water and O2.

pH. A logarithmic quantity that indicates

the acidity of a solution, that is, the concentration of hydronium ions in solution. pH is

defined as the negative logarithm of the hydronium ion concentration.

pH optimum. In an enzyme-catalyzed reaction, the pH at the point of maximum

catalytic activity.

phage. See bacteriophage.

phase-transition temperature (Tm). The

midpoint of the temperature range in which

lipids or other macromolecular aggregates

are converted from a highly ordered phase or

state (such as a gel) to a less-ordered state

(such as a liquid crystal).

F (phi). The angle of rotation around the

bond between the a-carbon and the nitrogen

of a peptide group.

phosphagen. A “high energy” phosphate

storage molecule found in animal muscle

cells. Phosphagens are phosphoamides and

have a higher phosphoryl-group-transfer

potential than ATP.

phosphatase. An enzyme that catalyzes

the hydrolytic removal of a phosphoryl


phosphatidate. A glycerophospholipid that

consists of two fatty acyl groups esterified to

C-1 and C-2 of glycerol 3-phosphate. Phosphatidates are metabolic intermediates in the

biosynthesis or breakdown of more complex


phosphoanhydride. A compound formed

by condensation of two phosphate groups.

phosphodiester linkage. A linkage in nucleic

acids and other molecules in which two alcoholic hydroxyl groups are joined through a

phosphate group.

phosphoester linkage. The bond by which a

phosphoryl group is attached to an alcoholic

or phenolic oxygen.

phospholipid. A lipid containing a phosphate moiety.

phosphorolysis. Cleavage of a bond within

a molecule by group transfer to an oxygen

atom of phosphate.

phosphorylase. An enzyme that catalyzes

the cleavage of its substrate(s) via nucleophilic attack by inorganic phosphate (Pi)

(i.e., via phosphorolysis).

phosphorylation. A reaction involving the

addition of a phosphoryl group to a molecule.

phosphoryl group transfer potential. A

measure of the ability of a compound to

transfer a phosphoryl group to another compound. Under standard conditions, group

transfer potentials have the same values as

the standard free energies of hydrolysis but

are opposite in sign.

photoautotroph. A photosynthetic organism that can utilize CO2 as its main carbon


photon. A quantum of light energy.

photophosphorylation. The light-dependent

formation of ATP from ADP and Pi catalyzed

by chloroplast ATP synthase.

photoheterotroph. Photosynthetic organism that requires organic molecules as a carbon source.

photoreactivation. The direct repair of

damaged DNA by an enzyme that is activated

by visible light.

photorespiration. The light-dependent uptake of O2 and the subsequent metabolism of

phosphoglycolate that occurs primarily in C3

photosynthetic plants. Photorespiration can

occur because O2 competes with CO2 for

the active site of ribulose 1,5-bisphosphate

carboxylase-oxygenase, the enzyme that catalyzes the first step of the reductive pentose

phosphate cycle.

photosynthesis. The conversion of light energy (photons) to chemical energy in the

form of ATP and/or NADPH.

photosystem. A functional unit of the lightdependent electron-transfer reactions of

photosynthesis. Each membrane-embedded

photosystem contains a reaction center, which

forms the core of the photosystem, and a pool

of light-absorbing antenna pigments.

phototroph. An organism that can convert

light energy into chemical potential energy

(i.e., an organism capable of photosynthesis).

physiological pH. The normal pH of human

blood, which is 7.4.

pI. See isoelectric point.

ping-pong reaction. A reaction in which an

enzyme binds one substrate and releases a

product, leaving a substituted enzyme that

then binds a second substrate and releases a

second product, thereby restoring the enzyme to its original form.

pitch. The axial distance for one complete

turn of a helical structure.

pKa. A logarithmic value that indicates the

strength of an acid. pKa is defined as the


negative logarithm of the acid dissociation

constant, Ka.

plasma membrane. The membrane that

surrounds the cytoplasm of a cell and thus

defines the perimeter of the cell.

plasmalogen. A glycerophospholipid that

has a hydrocarbon chain linked to C-1 of

glycerol 3-phosphate through a vinyl ether

linkage. Plasmalogens are found in the central nervous system and in peripheral nerve

and muscle tissue.

plasmid. A relatively small, extrachromosomal DNA molecule that is capable of autonomous replication. Plasmids are usually

closed, circular, double-stranded DNA


P:O ratio. The ratio of molecules of ADP

phosphorylated to atoms of oxygen reduced

during oxidative phosphorylation.

polar. Having uneven distribution of charge.

A molecule or functional group is polar if its

center of negative charge does not coincide

with its center of positive charge.

poly A tail. A stretch of polyadenylate, up to

250 nucleotide residues long, that is added to

the 3¿ end of a eukaryotic mRNA molecule

following transcription.

polyacrylamide gel electrophoresis (PAGE).

A technique used to separate molecules of

different net charge and/or size based on

their migration through a highly cross-linked

gel matrix in an electric field.

polycistronic mRNA. An mRNA molecule

that contains multiple coding regions. Many

prokaryotic mRNA molecules are polycistronic.

polymerase chain reaction (PCR). A

method for amplifying the amount of DNA in

a sample and for enriching a particular DNA

sequence in a population of DNA molecules.

In the polymerase chain reaction, oligonucleotides complementary to the ends of the

desired DNA sequence are used as primers for

multiple rounds of DNA synthesis.

polynucleotide. A polymer of many (usually

more than 20) nucleotide residues linked by

phosphodiester bonds.

polypeptide. A polymer of many (usually

more than 20) amino acid residues linked by

peptide bonds.

polyribosome. See polysome.

polysaccharide. A polymer of many (usually

more than 20) monosaccharide residues

linked by glycosidic bonds. Polysaccharide

chains can be linear or branched.

polysome. The structure formed by the

binding of many translation complexes to a

large mRNA molecule. Also known as a


polyunsaturated fatty acid. An unsaturated

fatty acid with two or more carbon-carbon

double bonds.

pore. See channel.

posttranscriptional processing. RNA processing that occurs after transcription is




posttranslational modification. Covalent

modification of a protein that occurs after

synthesis of the polypeptide is complete.

prenylated protein. A lipid-anchored protein that is covalently linked to an isoprenoid

moiety via the sulfur atom of a cysteine

residue at the C-terminus of the protein.

primary structure. The sequence in which

residues are covalently linked to form a polymeric chain.

primary transcript. A newly synthesized

RNA molecule before processing.

primase. An enzyme in the primosome that

catalyzes the synthesis of short pieces of RNA

about 10 residues long. These oligonucleotides are the primers for synthesis of

Okazaki fragments.

primosome. A multiprotein complex, including primase and helicase in E. coli, that

catalyzes the synthesis of the short RNA

primers needed for discontinuous DNA synthesis of the lagging strand.

processive enzyme. An enzyme that remains bound to its growing polymeric

product through many polymerization steps

(cf., distributive enzyme).

prochiral atom. An atom with multiple substituents, two of which are identical. A

prochiral atom can become chiral when one

of the identical substituents is replaced.

prokaryote. An organism, usually a single

cell, which contains no nucleus or internal

membranes (cf., eukaryote).

promoter. The region of DNA where RNA

polymerase binds during transcription


prostaglandin. An eicosanoid that has a cyclopentane ring. Prostaglandins are metabolic regulators that act in the immediate

neighborhood of the cells in which they are


prosthetic group. A coenzyme that is tightly

bound to an enzyme. A prosthetic group, unlike a cosubstrate, remains bound to a specific site of the enzyme throughout the

catalytic cycle of the enzyme.

protease. An enzyme that catalyzes hydrolysis of peptide bonds. The physiological substrates of proteases are proteins.

protein. A biopolymer consisting of one or

more polypeptide chains. The biological

function of each protein molecule depends

not only on the sequence of covalently linked

amino acid residues, but also on its threedimensional structure (conformation).

protein coenzyme. A protein that does not

itself catalyze reactions but is required for the

action of certain enzymes.

protein glycosylation. The covalent addition

of carbohydrate to proteins. In N-glycosylation, the carbohydrate is attached to the

amide group of the side chain of an asparagine residue. In O-glycosylation, the carbohydrate is attached to the hydroxyl group of

the side chain of a serine or threonine residue.

protein kinase. See kinase.

protein phosphatase. See phosphatase.

proteoglycan. A complex of protein with

glycosaminoglycan chains covalently bound

through their anomeric carbon atoms. Up to

95% of the mass of a proteoglycan may be


proteomics. The study of all proteins produced in a certain cell type, tissue, organ, or


protonmotive force (≤p). The energy

stored in a proton concentration gradient

across a membrane.

proximity effect. The increase in the rate of

a nonenzymatic or enzymatic reaction attributable to high effective concentrations of reactants, which result in more frequent

formation of transition states.

pseudo first-order reaction. A multi-reactant

reaction carried out under conditions where

the rate depends on the concentration of only

one reactant.

pseudogene. A nonexpressed sequence of

DNA that evolved from a protein-encoding

gene. Pseudogenes often contain mutations

in their coding regions and cannot produce

functional proteins.

C (psi). The angle of rotation around the

bond between the a-carbon and the carbonyl

carbon of a peptide group.

≤C . See membrane potential.

P site. Peptidyl site. The site on a ribosome

that is occupied during protein synthesis by a

tRNA molecule attached to the growing

polypeptide chain (peptidyl tRNA).

purine. A nitrogenous base having a tworing structure in which a pyrimidine is fused

to imidazole. Adenine and guanine are substituted purines found in both DNA and RNA.

pyranose. A monosaccharide structure that

forms a six-membered ring as a result of intramolecular hemiacetal formation.

pyrimidine. A nitrogenous base having a

heterocyclic ring that consists of four carbon

atoms and two nitrogen atoms. Cytosine,

thymine, and uracil are substituted pyrimidines found in nucleic acids (cytosine in

DNA and RNA, uracil in RNA, and thymine

principally in DNA).

Q. See mass action ratio.

Q cycle. A cyclic pathway proposed to explain

the sequence of electron transfers and proton

movements within Complex III of mitochondria or the cytochrome bf complex in chloroplasts. The net result of the two steps of the

Q cycle is oxidation of two molecules of QH2

or plastoquinol (PQH2); formation of one

molecule of QH2 or PQH2; transfer of two

electrons; and net translocation of four protons across the inner mitochondrial membrane to the intermembrane space or across

the thylakoid membrane to the lumen.

quaternary structure. The organization of

two or more polypeptide chains within a

multisubunit protein.

R state. The more active conformation of an

allosteric protein; opposite of T state.

Ramachandran plot. A plot of c versus f values for amino acid residues in a polypeptide

chain. Certain f and c values are characteristic of different conformations.

random sequential reaction. A reaction in

which neither the binding of substrates to an

enzyme nor the release of products from the

enzyme follows an obligatory order.

rate acceleration. The ratio of the rate constant for a reaction in the presence of enzyme

(kcat) divided by the rate constant for that reaction in the absence of enzyme (kn). The

rate acceleration value is a measure of the efficiency of an enzyme.

rate equation. An expression of the observed

relationship between the velocity of a reaction

and the concentration of each reactant.

rate determining step. The slowest step in a

chemical reaction. The rate determining step

has the highest activation energy among the

steps leading to formation of a product from

the substrate.

reaction center. A complex of proteins, electron transport cofactors, and a special pair

of chlorophyll molecules that forms the

core of a photosystem. The reaction center

is the site of conversion of photochemical

energy to electrochemical energy during


reaction mechanism. The step-by-step

atomic or molecular events that occur during

chemical reactions.

reaction order. See kinetic order.

reaction specificity. The lack of formation

of wasteful by-products by an enzyme. Reaction specificity results in essentially 100%

product yields.

reactive center. The part of a coenzyme to

which mobile metabolic groups are attached.

reading frame. The sequence of nonoverlapping codons of an mRNA molecule that specifies the amino acid sequence. The reading

frame of an mRNA molecule is determined by

the position where translation begins; usually

an AUG codon.

receptor. A protein that binds a specific

ligand, such as a hormone, leading to some

cellular response.

recombinant DNA. A DNA molecule that

includes DNA from different sources.

recombination. See genetic recombination.

reducing agent. A substance that loses electrons in an oxidation-reduction reaction and

thereby becomes oxidized.

reducing end. The residue containing a free

anomeric carbon in a polysaccharide. A polysaccharide usually contains no more than

one reducing end.

reduction. The gain of electrons by a substance through transfer from another substance (the reducing agent). Reductions can

take several forms, including the loss of oxygen from a compound, the addition of


hydrogen to a double bond of a compound,

or a decrease in the valence of a metal ion.

reduction potential (E). A measure of the

tendency of a substance to reduce other substances. The more negative the reduction potential, the greater the tendency to donate


regulated enzyme. An enzyme located at a

critical point within one or more metabolic

pathways, whose activity may be increased or

decreased based on metabolic demand. Most

regulated enzymes are oligomeric.

regulatory protein. A protein that is involved in the regulation of gene expression,

usually at the point of transcription initiation. Repressors and activators are examples

of regulatory proteins.

regulatory site. A ligand-binding site in a

regulatory enzyme distinct from the active

site. Allosteric modulators alter enzyme activity by binding to the regulatory site. Also

known as an allosteric site.

relative molecular mass (Mr). The mass of a

molecule relative to 1/12th the mass of 12C.

There are no units associated with the values

for relative molecular mass.

release factor. A protein involved in terminating protein synthesis.

renaturation. The restoration of the native

conformation of a biological macromolecule,

usually resulting in restoration of biological


replication. The duplication of doublestranded DNA, during which parental strands

separate and serve as templates for synthesis

of new strands. Replication is carried out by

DNA polymerase and associated factors.

replication fork. The Y-shaped junction

where double-stranded, template DNA is

unwound and new DNA strands are synthesized during replication.

replisome. A multiprotein complex that includes DNA polymerase, primase, helicase,

single-strand binding protein, and additional

components. The replisomes, located at each

of the replication forks, carry out the polymerization reactions of bacterial chromosomal DNA replication.

repressor. A regulatory DNA-binding protein that prevents transcription by RNA


residue. A single component within a polymer. The chemical formula of a residue is

that of the corresponding monomer minus

the elements of water.

resonance energy transfer. A form of excitation energy transfer between molecules

that does not involve transfer of an electron.

respiratory electron transport chain. A

series of enzyme complexes and associated

cofactors that are electron carriers, passing

electrons from reduced coenzymes or

substrates to molecular oxygen (O2), the

terminal electron acceptor of aerobic


restriction endonuclease. An endonuclease

that catalyzes the hydrolysis of double-stranded DNA at a specific nucleotide sequence.

Type I restriction endonucleases catalyze both

the methylation of host DNA and the cleavage

of nonmethylated DNA, whereas type II restriction endonucleases catalyze only the

cleavage of nonmethylated DNA.

restriction map. A diagram showing the size

and arrangement of fragments produced

from a DNA molecule by the action of various restriction endonucleases.

reverse transcriptase. A type of DNA polymerase that catalyzes the synthesis of a strand

of DNA from an RNA template.

reverse turn. See turn.

ribonucleic acid (RNA). A polymer consisting of ribonucleotide residues joined by

3¿ – 5¿ phosphodiester bonds. The sugar moiety in RNA is ribose. Genetic information

contained in DNA is transcribed in the synthesis of RNA, some of which (mRNA) is

translated in the synthesis of protein.

ribonucleoprotein. A complex containing

both ribonucleic acid and protein.

ribosome. A large ribonucleoprotein complex composed of multiple ribosomal RNA

molecules and proteins. Ribosomes are the

site of protein synthesis.

ribozyme. An RNA molecule with enzymatic


rise. The distance between one residue and

the next along the axis of a helical macromolecule.

RNA processing. The reactions that transform a primary RNA transcript into a mature RNA molecule. The three general types

of RNA processing include the removal of

RNA nucleotides from primary transcripts,

the addition of RNA nucleotides not encoded by the gene, and the covalent modification of bases.

rRNA. See ribosomal ribonucleic acid.

S. See Svedberg unit.

S. See entropy.

salt bridge. See charge-charge interactions.

salvage pathway. A pathway in which a

major metabolite, such as a purine or pyrimidine nucleotide, can be synthesized from a

preformed molecular entity, such as a purine

or pyrimidine.

saturated fatty acid. A fatty acid that does

not contain a carbon-carbon double bond.

Schiff base. A complex formed by the reversible condensation of a primary amine

with an aldehyde (to form an aldimine) or a

ketone (to form a ketimine).

SDS-PAGE. See sodium dodecyl sulfate–polyacrylamide gel electrophoresis.

second messenger. A compound that acts

intracellularly in response to an extracellular


secondary structure. The regularities in

local conformations within macromolecules.


In proteins, secondary structure is maintained by hydrogen bonds between carbonyl

and amide groups of the backbone. In nucleic acids, secondary structure is maintained by

hydrogen bonds and stacking interactions

between the bases.

second-order reaction. A reaction whose

rate depends on the concentrations of two reactants.

self-splicing intron. An intron that is excised in a reaction mediated by the RNA precursor itself.

sense strand. In double-stranded DNA the

sense strand is the strand that contains

codons. Also called the coding strand. The

opposite strand is called the antisense strand

or the template strand.

sequential reaction. An enzymatic reaction in which all the substrates must be

bound to the enzyme before any product is


sequential theory of cooperativity and allosteric regulation. A model of the cooperative binding of identical ligands to oligomeric

proteins. According to the simplest form of

the sequential theory, the binding of a ligand

may induce a change in the tertiary structure

of the subunit to which it binds and may

alter the conformations of neighboring subunits to varying extents. Only one subunit

conformation has a high affinity for the

ligand. Also known as the ligand-induced


Shine-Dalgarno sequence. A purine-rich

region just upstream of the initiation codon

in prokaryotic mRNA molecules. The ShineDalgarno sequence binds to a pyrimidinerich sequence in the ribosomal RNA, thereby

positioning the ribosome at the initiation


S factor. See s subunit.

S subunit (sigma subunit). A subunit of

prokaryotic RNA polymerase, which acts as a

transcription initiation factor by binding to

the promoter. Different s subunits are specific for different promoters. Also known as a

s factor.

signal peptidase. An integral membrane

protein of the endoplasmic reticulum that

catalyzes cleavage of the signal peptide of

proteins translocated to the lumen.

signal peptide. The N-terminal sequence of

residues in a newly synthesized polypeptide

that targets the protein for translocation

across a membrane.

signal transduction. The process whereby

an extracellular signal is converted to an intracellular signal by the action of a membrane-associated receptor, a transducer, and

an effector enzyme.

signal recognition particle (SRP). A eukaryotic protein-RNA complex that binds a

newly synthesized peptide as it is extruded

from the ribosome. The signal-recognition

particle is involved in anchoring the ribosome to the cytosolic face of the endoplasmic



reticulum so that protein translocation to the

lumen can occur.

single-strand binding protein (SSB). A protein that binds tightly to single-stranded

DNA, preventing the DNA from folding back

on itself to form double-stranded regions.

site-directed mutagenesis. An in vitro procedure by which one particular nucleotide

residue in a gene is replaced by another, resulting in production of an altered protein


site-specific recombination. An example of

recombination that occurs at specific sites in

the genome.

small nuclear ribonucleoprotein (snRNP).

An RNA-protein complex composed of one

or two specific snRNA molecules plus a number of proteins. snRNPs are involved in splicing mRNA precursors and in other cellular


small RNA. A class of RNA molecules. Some

small RNA molecules have catalytic activity.

Some small nuclear RNA molecules (snRNA)

are components of small nuclear ribonucleoproteins (snRNPs).

snRNA. See small nuclear RNA.

snRNP. See small nuclear ribonucleoprotein.

sodium dodecyl sulfate–polyacrylamide gel

electrophoresis (SDS-PAGE). Polyacrylamide

gel electrophoresis performed in the presence

of the detergent sodium dodecyl sulfate. SDSPAGE allows separation of proteins on the

basis of size only rather than charge and size.

solvation. A state in which a molecule or ion

is surrounded by solvent molecules.

solvation sphere. The shell of solvent molecules that surrounds an ion or solute.

special pair. A specialized pair of chlorophyll molecules in reaction centers that is the

primary electron donor during the light-dependent reactions of photosynthesis.

specific heat. The amount of heat required

to raise the temperature of 1 gram of a substance by 1°C.

specificity constant. See kcat>Km.

sphingolipid. An amphipathic lipid with a

sphingosine (trans-4-sphingenine) backbone. Sphingolipids, which include sphingomyelins, cerebrosides, and gangliosides, are

present in plant and animal membranes and

are particularly abundant in the tissues of the

central nervous system.

sphingomyelin. A sphingolipid that consists

of phosphocholine attached to the C-1 hydroxyl group of a ceramide. Sphingomyelins

are present in the plasma membranes of most

mammalian cells and are a major component

of myelin sheaths.

splice site. The conserved nucleotide sequence surrounding an exon-intron junction.

It includes the site where the RNA molecule is

cleaved during intron excision.

spliceosome. The large protein-RNA complex that catalyzes the removal of introns from

mRNA precursors. The spliceosome is composed of small nuclear ribonucleoproteins.

splicing. The process of removing introns

and joining exons to form a continuous RNA


SRP. See signal recognition particle.

SSB. See single-strand binding protein.

stacking interactions. The weak noncovalent

forces between adjacent bases or base pairs in

single-stranded or double-stranded nucleic

acids, respectively. Stacking interactions contribute to the helical shape of nucleic acids.

standard Gibbs free energy change (≤G° œ ).

The free energy change for a reaction under

biochemical standard state conditions.

standard reduction potential (E° œ ). A

measure of the tendency of a substance to reduce other substances under biochemical

standard state conditions.

standard state. A set of reference conditions

for a chemical reaction. In biochemistry, the

standard state is defined as a temperature of

298 K (25°C), a pressure of 1 atmosphere, a

solute concentration of 1.0 M, and a pH of 7.0.

starch. A homopolymer of glucose residues

that is a storage polysaccharide in plants.

There are two forms of starch: amylose, an

unbranched polymer of glucose residues

joined by a-(1 : 4) linkages; and amylopectin, a branched polymer of glucose

residues joined by a-(1 : 4) linkages with

a-(1 : 6) linkages at branch points.

steady state. A state in which the rate of synthesis of a compound is equal to its rate of

utilization or degradation.

stem-loop. See hairpin.

stereoisomers. Compounds with the same

molecular formula but different spatial

arrangements of their atoms.

stereospecificity. The ability of an enzyme

to recognize and act upon only a single

stereoisomer of a substrate.

steroid. A lipid containing a fused, four-ring

isoprenoid structure.

sterol. A steroid containing a hydroxyl group.

stomata. Structures on the surface of a leaf

through which carbon dioxide diffuses directly into photosynthetic cells.

stop codon. See termination codon.

strand invasion. The exchange of single

strands of DNA from two nicked molecules

having homologous nucleotide sequences.

stroma. The interior of a chloroplast corresponding to the cytoplasm of the ancestral


stromal lamellae. Regions of the thylakoid

membrane that are in contact with the stroma.

substrate. A reactant in a chemical reaction.

In enzymatic reactions, substrates are specifically acted upon by enzymes, which catalyze

the conversion of substrates to products.

substrate cycle. A pair of opposing reactions

that catalyzes a cycle between two pathway


substrate level phosphorylation. Phosphorylation of a nucleoside diphosphate by

transfer of a phosphoryl group from a nonnucleotide substrate.

supercoil. A topological arrangement assumed

by over- or underwound double-stranded DNA.

Underwinding gives rise to negative supercoils;

overwinding produces positive supercoils.

supersecondary structure. See motif.

Svedberg unit (S). A unit of 10 - 13 second

used for expressing the sedimentation coefficient, a measure of the rate at which a large

molecule or particle sediments in an ultracentrifuge. Large S values usually indicate

large masses.

symport. The cotransport of two different

species of ions or molecules in the same direction across a membrane by a transport protein.

synonymous codons. Different codons that

specify the same amino acid.

synthase. A common name for an enzyme,

often a transferase, that catalyzes a synthetic


synthetase. An enzyme that catalyzes the joining of two substrates and requires the input of

the chemical potential energy of a nucleoside

triphosphate. Synthetases are members of the

IUBMB class of enzymes known as ligases.

T state. The less active conformation of an

allosteric protein; opposite of R state.

TATA box. An A/T-rich DNA sequence

found within the promoter of both prokaryotic and eukaryotic genes.

template strand. The strand of DNA within

a gene whose nucleotide sequence is complementary to that of the transcribed RNA. During transcription, RNA polymerase binds to

and moves along the template strand in the

3¿ : 5¿ direction, catalyzing the synthesis of

RNA in the 5¿ : 3¿ direction.

termination codon. A codon that is recognized by specific proteins that cause newly

synthesized peptides to be released from the

translation machinery thus terminating

translation. The three termination codons

(UAG, UAA, and UGA) are also known as

stop codons.

termination sequence. A sequence at the 3 ¿

end of a gene that mediates transcription


tertiary structure. The compacting of polymeric chains into one or more domains within a macromolecule. In proteins, tertiary

structure is stabilized mainly by hydrophobic

interactions between side chains.

thermodynamics. The branch of physical

science that studies transformations of heat

and energy.

30 nm fiber. A chromatin structure in which

nucleosomes are coiled into a solenoid 30 nm

in diameter.

؊35 region. A sequence found within the

promoter of some prokaryotic genes about

30 to 35 base pairs upstream of the transcription initiation site.


310 helix. A secondary structure of proteins,

consisting of a helix in which the carbonyl

oxygen of each amino acid residue (residue

n) forms a hydrogen bond with the amide hydrogen of the third residue further toward

the C-terminus of the polypeptide chain

(residue n + 3).

thylakoid lamella. See thylakoid membrane.

thylakoid membrane. A highly folded, continuous membrane network suspended in

the aqueous matrix of the chloroplast. The

thylakoid membrane is the site of the lightdependent reactions of photosynthesis,

which lead to the formation of NADPH and

ATP. Also known as the thylakoid lamella.

Tm. See melting point and phase-transition


topoisomerase. An enzyme that alters the

supercoiling of a DNA molecule by cleaving a

phosphodiester linkage in either one or both

strands, rewinding the DNA, and resealing

the break. Some topoisomerases are also

known as DNA gyrases.

topology. 1. The arrangement of membranespanning segments and connecting loops in

an integral membrane protein. 2. The overall

morphology of a nucleic acid molecule.

TCC arm. The stem-and-loop structure in a

tRNA molecule that contains the sequence



trace element. An element required in very

small quantities by living organisms. Examples include copper, iron, and zinc.

transaminase. An enzyme that catalyzes the

transfer of an amino group from an a-amino

acid to an a-keto acid. Transaminases require

the coenzyme pyridoxal phosphate. They are

also called aminotransferases.

transcription. The copying of biological information from a double-stranded DNA

molecule to a single-stranded RNA molecule,

catalyzed by a transcription complex consisting of RNA polymerase and associated


transcription bubble. A short region of

double-stranded DNA that is unwound by

RNA polymerase during transcription.

transcription factor. A protein that binds to

the promoter region, to RNA polymerase, or

to both during assembly of the transcription

initiation complex. Some transcription

factors remain bound during RNA chain


transcription initiation complex. The complex of RNA polymerase and other factors

that assembles at the promoter at the start of


transcriptional activator. A regulatory DNAbinding protein that enhances the rate of

transcription by increasing the activity of

RNA polymerase at specific promoters.

transducer. The component of a signaltransduction pathway that couples receptorligand binding with generation of a second

messenger catalyzed by an effector enzyme.

transfer ribonucleic acid. See tRNA.

transferase. An enzyme that catalyzes a

group-transfer reaction. Transferases often

require a coenzyme.

transition state. An unstable, high-energy

arrangement of atoms in which chemical

bonds are being formed or broken. Transition states have structures between those of

the substrates and the products of a reaction.

transition-state analog. A compound that

resembles a transition state. Transition-state

analogs characteristically bind extremely

tightly to the active sites of appropriate enzymes and thus act as potent inhibitors.

transition-state stabilization. The increased

binding of transition states to enzymes relative

to the binding of substrates or products. Transition-state stabilization lowers the activation

energy and thus contributes to catalysis.

translation. The synthesis of a polypeptide

whose sequence reflects the nucleotide sequence of an mRNA molecule. Amino acids

are donated by activated tRNA molecules,

and peptide bond synthesis is catalyzed by

the translation complex, which includes the

ribosome and other factors.

translation complex. The complex of a ribosome and protein factors that carries out

the translation of mRNA in vivo.

translation initiation complex. The complex

of ribosomal subunits, an mRNA template, an

initiator tRNA molecule, and initiation factors

that assembles at the start of protein synthesis.

translation initiation factor. A protein involved in the formation of the initiation

complex at the start of protein synthesis.

translocation. 1. The movement of the ribosome by one codon along an mRNA molecule. 2. The movement of a polypeptide

through a membrane.

transposon. A mobile genetic element that

jumps between chromosomes or parts of a

chromosome by taking advantage of recombination mechanisms. Also known as a transposable element.

transverse diffusion. The passage of lipid or

protein molecules from one leaflet of a lipid

bilayer to the other leaflet. Unlike lateral diffusion within one leaflet of a bilayer, transverse diffusion is extremely slow.

triacylglycerol. A lipid containing three

fatty acyl residues esterified to glycerol. Fats

and oils are mixtures of triacylglycerols. Formerly known as a triglyceride.

tricarboxylic acid cycle. See citric acid cycle.

triglyceride. See triacylglycerol.

triose. A three-carbon sugar.

tRNA. A class of RNA molecules that carry

activated amino acids to the site of protein

synthesis for incorporation into growing

peptide chains. tRNA molecules contain an

anticodon that recognizes a complementary

codon in mRNA.

turn (in proteins). A protein loop of 4-5

residues that causes a change in the direction

of a polypeptide chain in a folded protein.


turnover. The dynamic metabolic steady

state in which molecules are degraded and replaced by newly synthesized molecules.

turnover number. See catalytic constant.

twist. The angle of rotation between adjacent residues within a helical macromolecule.

type I reaction center. The special pair of

chlorophyll molecules and associated electron transfer chain found in photosystem I.

type II reaction center. The reaction center

found in photosystem II.

uncompetitive inhibition. Inhibition of an

enzyme-catalyzed reaction by a reversible inhibitor that binds only to the enzyme-substrate complex, not to the free enzyme.

uncouplers. See uncoupling agent.

uncoupling agent. A compound that disrupts the usual tight coupling between electron transport and phosphorylation of ADP.

uniport. The transport of a single type of

solute across a membrane by a transport


unsaturated fatty acid. A fatty acid with at

least one carbon-carbon double bond. An unsaturated fatty acid with only one carbon-carbon double bond is called a monounsaturated

fatty acid. A fatty acid with two or more carbon-carbon double bonds is called a polyunsaturated fatty acid. In general, the double

bonds of unsaturated fatty acids are of the cis

configuration and are separated from each

other by methylene ( ¬ CH2 ¬ ) groups.

urea cycle. A metabolic cycle consisting of

four enzyme-catalyzed reactions that converts nitrogen from ammonia and aspartate

to urea. Four ATP equivalents are consumed

during formation of one molecule of urea.

v. See velocity.

v0. See initial velocity.

vacuole. A fluid-filled organelle in plant

cells that is a storage site for water, ions, or


van der Waals force. A weak intermolecular

force produced between neutral atoms by

transient electrostatic interactions. Van der

Waals attraction is strongest when atoms are

separated by the sum of their van der Waals

radii; strong van der Waals repulsion precludes closer approach.

van der Waals radius. The effective size of

an atom. The distance between the nuclei of

two nonbonded atoms at the point of maximal attraction is the sum of their van der

Waals radii.

variable arm. The arm of a tRNA molecule

that is located between the anticodon arm

and the TcC arm. The variable arm can range

in length from about 3 to 21 nucleotides.

velocity (V). The rate of a chemical reaction,

expressed as amount of product formed per

unit time.

very low density lipoprotein (VLDL). A

type of plasma lipoprotein that transports

endogenous triacylglycerols, cholesterol, and

cholesteryl esters from the liver to the tissues.

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10 Active Transport of ATP, ADP, and Pi Across the Mitochondrial Membrane

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